Commercial farming is a critical part of the economy. However crops are subject to near constant attack by insects, fungi, bacteria and other pathogens. When such pathogens encounter susceptible crops, such attacks can result in lower yield quality and can even destroy entire crops. Thus, pathogens cause substantial economic harm to growers and in some areas of the world contribute to famine.
Traditionally, farmers have relied upon conventional tillage methods to disrupt the soil and thereby control weeds, pathogens and volunteer crops. However, the current trend, particularly in the Pacific Northwest region, is to use no-till or direct seed crop production methods to reduce soil erosion and the accompanying environmental degradation associated with conventionally tilled fields. No-till and direct seeding methods aim to reduce environmental degradation but generally require the use of herbicides to control weeds and volunteer crops.
Typically growers apply herbicides prior to planting to control weeds since the crop itself may be susceptible to the herbicide. However the development of herbicide resistant wheat varieties raises the possibility of increasing wheat yields by applying the herbicide to the standing crop. Unfortunately, weeds dying in the standing crop have been demonstrated to result in carryover of fungal pathogens, which typically are unaffected by herbicides, from the dying weeds to the standing wheat crop. Indeed, U.S. Pat. No. 5,972,689 to Cook et al. (Cook) discloses that spraying with an herbicide such as glyphosate controls weeds, but favors the development of Rhizoctonia root rot in wheat. Because wheat is particularly susceptible to fungal pathogens, this carryover or “green-bridge” is a serious problem.
This green-bridge effect often leads to yield reductions associated with increased disease pressure which are the result of increased soilborne pathogens present on dying herbicide-sensitive volunteer and/or weeds. For example, R. solani significantly reduced grain yields of glyphosate-sensitive barley when glyphosate was applied three days before planting. However, no significant yield depression was detected when glyphosate was applied in the fall or three weeks prior to planting (Smiley et al. Plant Dis. 1992, 76, 937-942). These results demonstrate that a fresh source of R. solani inoculum, from the dying volunteer and weeds treated with glyphosate three days prior to planting, acted as a green-bridge for the fungus to infect barley planted shortly after herbicide application.
Another fungal disease of concern, take-all, is caused by Gaeumannomyces graminis var. tritici (Ggt), which has been a persistent pathogen plaguing wheat around the world for over a hundred years. Take-all (Ggt) disease is present in the roots, crown, and basal stem of infected wheat plants. Severe Ggt infection can decrease grain yields by as much as 50%. Symptoms of infection include stunting, blackened lower stems, and white heads. Take-all will commonly put out “runner-hyphae” to neighboring plants, so that a single site of infection is sufficient to cause multiple infections. Persistence through a green-bridge effect can occur similar to that reported for R. solani. Studies conducted in New Zealand have shown that treatment of cereals with glyphosate increases the levels of infection with Ggt due to the green-bridge effect of the herbicide on couch grass (Harvey et al. Aglink 1/3000/3/82, 1982, Ministries of Agriculture and Fisheries, Wellington, New Zealand). The most successful current form of Ggt control is through crop rotation, which is not always satisfactory for wheat production.
Nineteen Pythium species have been reported to be pathogenic to wheat roots. Pythium inoculum will remain active within the upper soil layer for years, utilizing residues as a source of nutrients. Pythium is considered to be a primary colonizer and infection levels can be reduced by removing straw and debris from the field. Unfortunately, this is not an option in a no-till system.
The interaction between glyphosate treated plants and infection by Pythium spp. has been investigated with numerous crop species. Soilborne Pythium spp. were found to be the first and predominant root colonizers of glyphosate treated plants (Levesque et al. Mycological Research 1993, 20, 307-312). This is an important observation since Pythium damage is often overlooked by growers, even though significant yield loss resulting from Pythium infection can occur.
Another group of important pathogens that affect wheat include foliar fungal pathogens, such rusts. Rust pathogens are parasitic fungi that infect wheat, barley, oats, beans, corn, sorghum, and other plants. Each rust pathogen is generally specific to its host and the location on the plant where infection occurs. The stem rust pathogen (Puccinia graminis f. sp. tritici) is a fungus that principally infects the leaf sheath of wheat plants. The leaf rust pathogen (Puccinia recondita f. sp. tritici) infects wheat plants through the stomates. The stripe rust pathogen (Puccinia striiformis) is similar to leaf rust, but differs in that infections appear systemic due to colonization patterns on wheat leaves.
Soybean rust is another serious rust pathogen that causes crop losses. It has not yet been detected in the continental United States, but the fact that it is principally spread by wind-borne spores indicates it may eventually reach major soybean growing areas in the United States. Soybean rust is caused by two fungal species, Phakopsora pachyrhizi and Phakopsora meibomiae. It has been reported in various countries including Australia, China, Korea, India, Japan, Nepal, Taiwan, Thailand, the Philippines, Mozambique, Nigeria, Rwanda, Uganda, Zimbabwe, South Africa, Brazil, Argentina, and Paraguay. P. meibomiae has been reported to be a weak pathogen. However, Phakopsora pachyrhizi is much more aggressive and recent introductions of P. pachyrhizi have rapidly spread causing severe damage in Zimbabwe, South Africa, Paraguay, and Brazil. Yield losses have been reported from 10-80%. Other important fungal pathogens that affect soybeans include root rot caused by various species of Phytophthora. 
There are few methods for controlling fungal diseases in wheat and soybeans, and none of these methods are widely accepted as being commercially viable. For example, some root rot diseases can be controlled through of crop rotation, that is, by not growing wheat in the same field more than every third or fourth year. However, like most other enterprises, agriculture has forced farmers to specialize in order to compete. The United States grows some 150 different crops, but fewer than 15 of these crops (including wheat and barley) occupy more than 90% of U.S. cropland, with the vast majority of farms specialized in the production of a single crop year after year on the same land, or two or at most three crops grown in a rotation on any given farm. Many wheat farms in areas well-suited to cereals tend to grow wheat every year or at least every other year in the same fields. Moreover, in certain regions, such as in the Pacific Northwest, leguminous crops commonly used in rotations do not bring the same levels of financial returns as do continuous wheat cropping systems (see, Cook and Veseth Wheat Health Management; American Phytopathological Society: St. Paul, Minn., 1991). Therefore, crop rotation is not a feasible economic solution to reduce disease pressure in a continuously cropped no-till production system.
Many diseases of wheat, barley, and other crops are controlled by breeding varieties of the crops with resistance to the pathogens. However, this approach has not worked for certain fungal diseases of wheat, particularly root diseases. No commercial wheat is available that has resistance to take-all, Rhizoctonia root rot, or Pythium root rot. Moreover, rust pathogens mutate at a relatively high rate, and therefore new rust-resistant cultivars of wheat are needed approximately every seven years.
Another method that is currently used to combat fungal infections is the topical application of fungicides. Fungicides, although effective, are prohibitively expensive for growers and typically must be applied as a preventative, even if it is not certain that the plants will be infected. Moreover many of the fungicides previously used have been withdrawn by the EPA. Compounds that are currently used are more easily degraded and therefore are less harmful to the environment, but fungi can quickly develop resistance to these compounds. Thus, fungicide applications are even less desirable than before.